Newest update of Toolbag has multiple material support per mesh. In the baking menu, you just click the box (multiple texture sets or something like that), pretty self explanatory from there. 

Needles said:

"Alright, so I've decided I want to become a concept artist ..."

New version Fast PBR Materials v1.1.0 is out!

Good day. Project still in wip stage, but there are a lot of ingame shots, fixes, etc.

ant1fact said:

Firstly, A+ on actually testing shit because nothing made sense. It's a thrill to help you.

I'm running into some quirks (maybe bugs?) and would love some better understanding. Sorry in advance if any or all of this has already been covered.

Looks like you are using Maya LT which explains the simplified shape node. 

Hello all!